Data Quality Assessment Report
massqc from tidymass by Xiaotao Shen
2022-03-06
PARAMETERS
Table 1: Parameter setting
| pacakge_name | function_name | parameter | time |
|---|---|---|---|
| massprocesser | process_data | path:~/scratch60 | 2022-02-28 13:05:44 |
| massprocesser | process_data | polarity:negative | 2022-02-28 13:05:44 |
| massprocesser | process_data | ppm:20 | 2022-02-28 13:05:44 |
| massprocesser | process_data | peakwidth:5,30 | 2022-02-28 13:05:44 |
| massprocesser | process_data | snthresh:10 | 2022-02-28 13:05:44 |
| massprocesser | process_data | prefilter:3,500 | 2022-02-28 13:05:44 |
| massprocesser | process_data | fitgauss:FALSE | 2022-02-28 13:05:44 |
| massprocesser | process_data | integrate:2 | 2022-02-28 13:05:44 |
| massprocesser | process_data | mzdiff:0.01 | 2022-02-28 13:05:44 |
| massprocesser | process_data | noise:500 | 2022-02-28 13:05:44 |
| massprocesser | process_data | threads:6 | 2022-02-28 13:05:44 |
| massprocesser | process_data | binSize:0.025 | 2022-02-28 13:05:44 |
| massprocesser | process_data | bw:5 | 2022-02-28 13:05:44 |
| massprocesser | process_data | output_tic:FALSE | 2022-02-28 13:05:44 |
| massprocesser | process_data | output_bpc:FALSE | 2022-02-28 13:05:44 |
| massprocesser | process_data | output_rt_correction_plot:FALSE | 2022-02-28 13:05:44 |
| massprocesser | process_data | min_fraction:0.5 | 2022-02-28 13:05:44 |
| massprocesser | process_data | fill_peaks:FALSE | 2022-02-28 13:05:44 |
| massdataset | create_mass_dataset() | no:no | 2022-02-28 14:07:06 |
| massdataset | mutate() | parameter_1:batch=as.character(batch) | 2022-03-06 09:17:58 |
| massdataset | mutate() | parameter_1:batch=as.character(batch) | 2022-03-06 09:18:54 |
SAMPLE INFORMATION
#> --------------------
#> massdataset version: 0.99.4
#> --------------------
#> 1.expression_data:[ 6557 x 299 data.frame]
#> 2.sample_info:[ 299 x 6 data.frame]
#> 3.variable_info:[ 6557 x 3 data.frame]
#> 4.sample_info_note:[ 6 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> --------------------
#> Processing information (extract_process_info())
#> create_mass_dataset ----------
#> Package Function.used Time
#> 1 massdataset create_mass_dataset() 2022-02-28 14:07:06
#> process_data ----------
#> Package Function.used Time
#> 1 massprocesser process_data 2022-02-28 13:05:44
#> mutate ----------
#> Package Function.used Time
#> 1 massdataset mutate() 2022-03-06 09:17:58
#> 2 massdataset mutate() 2022-03-06 09:18:54
Figure 1: Peak intensity profile.
MISSING VALUES
MISSING VALUES IN DATASET
Black is MV.
Figure 2: Missing values in dataset
MISSING VALUES IN VARIABLES
Figure 3: Missing values in variables
MISSING VALUES IN SAMPLES
Figure 4: Missing values in samples
RSD DISTRIBUTATION
Figure 5: RSD distributation
INTENSITY FOR ALL THE VARIABLES
Figure 6: Intensity for all the variables
SAMPLE CORRELATION
Figure 7: Sample correlation
PCA score plot
